Pokemon: Rocket's Reign
by Bioniclefan234
Summary: Team Rocket has won. The world belongs to them. And only one boy can stop them from completing their plan. Rated T for language and bloody references.  Disclaimer: I do not own Pokemon, nor am I affiliated with Nintendo or Gamefreak.
1. Prologue

**Prologue**

_I, Giovanni…_

"Charizard, use Flamethrower!"

Gary watched as the Pokemon launched a flame from its mouth, aiming for the purple Pokemon nearby. It glared with cold eyes as the attack hit, but shrugged it off as though it was nothing. Gary stared in disbelief as the Pokemon simply gestured and sent Charizard crashing into a wall, knocking it out instantly.

…_leader of Team Rocket…_

The Pokemon turned to face the three Gym Leaders behind it: Misty of Cerulean City, Brock of Pewter City, and Roxanne of Rustboro City. It narrowed its eyes, raised an arm, and squeezed its hand. The Gym Leaders couldn't even scream as their necks were instantly shattered.

…_am armed with the world's strongest Pokemon…_

Lance and Clair sent out their Dragonite, who both glared at the opponent. The Pokemon turned and examined its opponents. It then shrugged and gestured, sending the Dragon-types crashing into their Trainers. Clair's was unconscious, but Lance's attempted to rise. A simple blast of power from the Pokemon's outstretched hand knocked it out.

…_and an army of people who are completely loyal to me._

Leaf growled and sent out her Houndoom, who growled at the Pokemon. The Pokemon, without even turning to face it, gestured at Houndoom and sent it flying into the air. It landed at its Trainer's feet, completely beaten.

_Nothing can stand against me._

Everyone gathered near their beaten Pokemon and the corpses of their deceased friends. Well, almost everyone. One man laughed manically as he walked beside Mewtwo and laid his hand on its shoulder.

_I have complete control of the Pokemon League systems. _

"Well done, Mewtwo. Now, finish them."

_I control the League. _

Mewtwo raised a hand and prepared its abilities to wipe out Giovanni's opponents.

_I control the world. _

Mewtwo smirked as the Trainers began backing way even as Team Rocket soldiers raced in and aimed their guns at them. They all turned and knew death was upon them.

_I am Giovanni…_

Leaf was the only won left alive after the shooting. Giovanni watched as she slumped to the ground, tears in her eyes. He approached her, saying, "You and your pathetic resistance have lost. With Mewtwo under my command, nothing can stop me. Why not join us, and share in our power? We could use someone of your power in our ranks."

Leaf took a deep breath and said, "Very well, Giovanni. I shall join Team Rocket."

…_AND I HAVE WON!_


	2. Chapter 1

**Chapter 1**

A lone man climbed the side of a mountain. On his shoulder rode a Pikachu, who observed its Trainer's damaged form. A scar was down the left side of his face, and blood was oozing from the side of his mouth. The man's legs, although they were covered by a pair of jeans, had many bruises, and his arms held many more.

"I…still can't believe I failed…" Red murmured as he hauled himself onto a ledge. He sat there, panting, as Pikachu leaped from his shoulder to check out the surroundings. Team Rocket had recently swept through the area and captured the majority of the Pokemon. Those that were left were in hiding.

"What can I do now?" Red said, mostly to himself. "The Gym Leaders and Elite Four are dead, and…and Leaf is now a Team Rocket Administrator. There's…there's no hope, is there, Pikachu?"

The little Pokemon put a comforting hand on Red's knee, smiling. It then leaped onto Red's shoulder as he began climbing again.

Recently, Red had been imprisoned in the Saffron City Kanto Prison after he had refused Giovanni's offer to join Team Rocket. He had been awaiting execution, his Pokemon held in suspended animation, when Sabrina appeared. She was among the last of the Gym Leaders, and had rescued Red and his Pokemon, ordering him to hide in Mount Silver. Red had done just that, evading Rocket hunter-killer teams and even fought Leaf near the Victory Road.

The battle had been harsh, but Red had prevailed. Leaf stepped aside and allowed Red to escape, saying that she might not be so merciful next time.

Red paused at the top of Mount Silver, where he could look over both Johto and Kanto. He had been here for a year before Gold and his team defeated him and sent him home.

"We're going to be spending a very long time here, pal," Red said to Pikachu. "We might as well get comfortable."

_Twelve years later…_

A young boy stretched as he exited his home in Pallet Town. The sun was rising as Team Rocket soldiers marched through the roads. There weren't a lot, just enough to make sure that no rebellions or riots formed here. They were still threatening, though.

The kid, whose name was Brad, wore a pair of black shoes and jeans, with a white shirt and a red and black cap styled somewhat like a PokeBall. He had green eyes, brown hair, and stood at about five feet, seven inches.

Several kids were playing nearby when one of them ran into the street and collided with a Rocket soldier. Brad decided to watch what was to happen.

"Oops! Sorry mister!" the kid said, smiling.

"You little prick!" the Soldier shouted, grabbing the kid's shirt and lifting him off the ground. "You dare run into me? A member of Team Rocket?"

The kid's eyes were filled with confusion and fear. His friends were too afraid to move, even think. Suddenly, a woman flew out of the door to a house, a Delcatty right behind her. She raced to the Soldier and snarled, "Get your filthy hands off of my child!"

The Soldier growled and punched the woman in the face, sending her to the ground. The Delcatty hissed, arching its back, but then the Soldier sent out his Toxicroak.

"Make sure it does not interfere while I deal punishment to these…offenders," the Soldier ordered, turning his attention back to the child in his hand.

"As for you, you little shit…" the Soldier raised his fist and smashed it into the child's face. Tears began to well up in the child's eyes as the Rocket threw him to the ground. He glared at everyone, turned, and left, the Toxicroak following him.

Brad sighed; such things weren't uncommon. Several years back, he had been punched in the gut for simply getting in the way of a Rocket patrol.

Brad walked to the nearby forest, where he would always head off into when he wanted to be alone. As he wandered, he spotted Flying-type Pokemon flying through the sky. According to his parents, ever since Team Rocket came to power, the four regions of Kanto, Johto, Hoenn, and Sinnoh went under drastic changes. For one, the Pokemon League had been disbanded. There were no more Gym Leaders, Elite Four, or Champions.

Next, Trainers now had to be approved by defeating a Rocket Mayor, which were appointed to watch over their appointed towns and hand out PokeBalls and Pokedexes to new Trainers. Those who failed to defeat the Mayors could not be allowed to catch any Pokemon besides the one they owned.

Suddenly, Brad heard a faint moan from somewhere nearby. He raced through the trees until he saw an injured Bagon lying on the ground. It looked up at him weakly and cried out.

Brad gently picked up the Bagon and held it. It looked as though it had been beaten, but that didn't matter. He raced back to Pallet Town, avoided the Rockets on patrol, and entered his home.

"Mom!" he shouted as soon as he stepped into the living room. "Dad!"

His parents raced over from the kitchen. His father was about six feet, two inches tall, with dark hair, a hard jaw, and strong muscles beneath his black business suit. His mother was only one inch taller than Brad, with green eyes, an orange dress, and red hair. Both looked worried when they saw the Bagon.

"Where did you find that, dear?" his mother asked.

"Out in the woods!" Brad answered. "It's badly injured!"

"Alright, take it to the kitchen. We'll heal it up there," his dad said. "We have some medical supplies in the cabinet."

**Okay, to clarify, this story takes place about twenty years after HG/SS. In case you're wondering, we will be seeing Unova and 5th**** Generation Pokemon, but not for quite a while. Team Rocket has not yet conquered it. Someone else has, but more on that later.**

**Also, here are the new ranks of the Team Rocket army after the conquest of the world:**

**Grunts-Same as the Games.**

**Administrators-Control the Grunts, but only have authority over small groups. **

**Executives-They control over all Administrators and Grunts. They have access to the Capitol Cities of Team Rocket in each region. However, they do not have as much control as…**

**Mayors-They have complete control of each city and the civilians and Rockets in them. They battle new Trainers to see if they are worthy of being able to travel and capture new Pokemon. However, some Mayors are given control over two cities/towns if one of them is too small for its own Mayor. An example is Viridian City-Pallet Town.**

**Presidents-There are a total of four, one to control each region. They are handpicked by Giovanni himself, and control every Mayor in the world. Only Giovanni commands them, and their Pokemon are extremely strong, so strong that only Giovanni can beat them in battle.**

**And…there you have it. Leaf will also be making an appearance in a later chapter, if you're curious. **


	3. Chapter 2

_Chapter 2_

_Brad paced endlessly in the living room as his parents fixed up the Bagon. It was nearly noon when his mother came out, smiling, and said, "The Bagon will be fine."_

_Brad was filled with joy. He raced over to the Bagon in the kitchen, where it was bandaged and smiling weakly. His father wasn't there, however, but Brad was happy that the Bagon was better._

_His mother approached and asked, "What will you do with it?"_

_Brad looked down at the Bagon and answered, "I…suppose I'll keep it, if it's alright with Bagon."_

_In reply, the Bagon leapt into Brad's arms. It hugged his neck as Brad laughed and hugged it back. His mother smiled and exited the room. She returned a moment later with a PokeBall in her hand. _

"_Here," she said, handing it to her son. Brad took it, and Bagon leaped into it. Once it was caught, Brad let it out again. _

"_What will you do now that you have a little Pokemon?" his mom asked._

"_Erm…" Brad hesitated. He had never thought he'd obtain a Pokemon, so he had never made plans for when he did get one. _

"_I suppose…I'll travel around. See the world."_

"_Then I wish you luck," his mother said. "Here, I'll help you pack."_

_-Line-_

_Several hours later, Brad exited Pallet Town's gate and walked through Route 1. Multiple Pokemon such as Rattata and Pidgey were found in the area, but Team Rocket's rules stated that he couldn't catch any of them. _

_Of course, he had no Pokemon anyway. _

_But that didn't stop him from training his Bagon along the way. _

_Eventually, he arrived at the gate to find a Trainer already standing there, nervously gazing at the large gate. It was a repaint of the gate that originally stood there, with black coloring and a large red "R" on top. Below that R was Team Rocket's slogan: "We fight. We kill. We take. We are your rulers, from now to eternity. We are Team Rocket."_

"_Hello!" Brad said in a friendly tone, his Bagon walking behind him. _

"_H-hi…" the Trainer, a young boy of about twelve years of age, replied. He had blonde hair and clothing that reminded Brad of the uniforms that Pokeathlon participants wore. _

"_What's your name?" Brad asked. _

"_S-Steve…"_

"_Do you want to battle?" Brad asked._

"_No. I'm not very good…"_

"_Are you okay?"_

"_I'm not sure."_

_With that, the boy raced into the gate. Brad heard shouting, some weeping, then silence. Brad entered to find a Team Rocket security guard there, a Growlithe beside him. _

_Brad mentally slapped himself. He had forgotten all about the security toll. Team Rocket charged people a $50 fine for entering and exiting a large city. _

_Brad checked his pockets and pulled out $50 and a note from his mother. It said:_

_Knew you'd forget about the toll, so I slipped this into your pocket. _

_-Love, Mom._

Brad handed the guard the money, who growled and allowed him to pass. Brad entered the city and the first thing he saw were the guards.

There were hundreds of them, roaming the streets, firearms in their hands, glaring at people they passed. Brad gulped, walked up into the city, and was immediately approached by about five Team Rocket Soldiers.

"You a Pokemon Trainer?" a large man asked.

"Yes," Brad answered, a little afraid. His Bagon growled and glared at Team Rocket.

"Good. Follow us."

Brad followed Team Rocket through the city, examining the great city around him. Aside from the guards, a great many people lived here, from little kids to old folk. Brad ignored their stares as he was brought before a large dark building with columns and large stairs before it. Brad glanced at the guards, one of whom said, "This is the Viridian City Mayor building. Mayor Zach should be inside. If you wish to be a proper Pokemon Trainer, you have to fight him."

Brad nodded and walked up into the building, his Bagon already prepared for battle.


	4. Chapter 3

**Chapter 3**

Brad entered the building and noticed that about twelve armed guards stood along the walls leading to the end of the hall, where a door was located. Brad tried to ignore them as he walked to the end, opened the door, and stepped inside.

He emerged into a large Pokemon battle field. The roof was closed, but large windows allowed sunlight to filter in. On the far end, a man stood, arms folded across his chest. He had short, dark hair, blue eyes, and large muscles beneath his business-style suit.

"So, you're my next challenger?" Mayor Zach said, sounding bored.

"Yep, and I'm gonna win!" Brad declared. His Bagon raced into the field, ready for battle.

Zach sighed. "Very well. Combee, take the field."

A small Pokemon with what appeared to be three heads in a sort of hexagonal pattern appeared, flying on short wings. It glared at Bagon, then looked bored. It had fought and defeated a Dratini, and doubted that a Bagon would be much different.

"You may have the first attack, child," Zach said.

"You'll regret that!" Brad said. "All right Bagon, start with Leer!"

Bagon made odd faces at Combee, which made the Bug-type chuckle and lowered its defense. Zach said and waved dismissively, knowing he had already won. "Combee, use Bug Bite."

Combee charged, its mouth opening in preparation for its attack. As green light appeared in its mouth, Brad ordered, "Bagon, dodge it!"

Bagon tried to move out of the way, but Combee was faster, grabbing onto Bagon's leg and biting down hard. It screamed and glared at Combee.

"Now, Gust to blow it away," Zach said.

The twin wings of the Combee began vibrating until they created a strong Gust to blow away Bagon. It landed at Brad's feet, weakened but still able to battle. It rose to its feet and glared at Combee. Zach was momentarily startled, but then shrugged. Bagon would soon be defeated, anyway.

"Bagon, charge and use Bite!" Brad ordered.

Bagon raced forth, leaping into the air to Bite its opponent. He was so intent on its attack that it failed to notice Combee flying out of the way until it crashed to the ground. Bagon tried to rise, but Combee used Gust to force it back down.

Brad grimaced. At this rate, he was going to lose! How could go home with that knowledge?

"Bagon, use Rage!" Brad ordered.

Bagon felt its anger rising as its Attack began increasing. It turned, glared at Combee, and lunged in for another Bite attack. It grabbed onto Combee, forced it to the ground, and then used another Bite to grab it in its mouth to throw it into the air so it could land at Zach's feet.

"My…my Combee…" Zach stammered in shock. He fell to his knees, than recalled the Bug-type. He looked up at Brad and growled, "My guards shall give you the Pokedex, PokeBalls, and TM Case. Now, leave."

Brad grabbed and hugged Bagon when it came racing over, and then exited the arena. He was approached by the guards, who gave him the items, then literally kicked him out of the building.

-Line-

After healing Bagon at the Pokemon Center, Brad left Viridian City and began exploring Viridian Forest. He had only begun exploring the Forest for about ten minutes before he realized something.

"I'm lost," he stated in shock. His Bagon frowned and kicked the ground.

"Well, I suppose that's not the worst thing that could happen, right?" Brad said to Bagon, smiling.

Without warning, about twelve Beedrill shot out from behind some trees. Brad and Bagon turned and ran, with Brad crying out, "OKAY, IT JUST GOT WORSE!"

-Line-

Giovanni paced endlessly in his office. His secretary had just reported to him about a secret organization forming somewhere in his territories, plotting the downfall of Team Rocket. Yes, Giovanni had dealt with several past resistance movements in the past, but what set this one apart was the fact that this resistance had been formed in secret for about ten years. _Ten years. _Right under _his _nose. And they were only just beginning minor operations against Team Rocket, such as spy missions and mysterious assassinations. Just yesterday Mayor Kelsey of Eterna City had to be replaced because she had been killed when a Voltorb used Self-Destruct to blow up her car.

A Rocket Executive, Proton, entered Giovanni's office and ignored the cold stare Mewtwo gave him from the corner of the room. He folded his hands across his chest and said, "Sir, Alpha Squad has just brought in Bill."

"Excellent. Bring the traitor here."

Proton nodded, exited, and reappeared a moment later, following two Rocket Grunts that were carrying a rather beaten man between them. They tossed him to the ground and moved to the walls, glaring at the man.

"Greetings, Bill," Giovanni greeted the prisoner, but his voice carried no warmth. "Do you know why you are here?"

"This bastard," Bill answered, gesturing at Proton, "said I have betrayed the Rocket Empire by conferring with rebels, when I have no knowledge of any sort."

Giovanni sighed. "We have intercepted an e-mail from you linking to somewhere in Hoenn. We know you have been conferring with these rebels. Where are they, and why would you risk your life?"

"Like I'd tell you," Bill growled.

Giovanni kicked Bill in the face, growling. "Haven't you heard of Mewtwo's torture methods? He uses his Psychic abilities to slip into your mind, search for your greatest fear, and creates a never-ending illusion of it. Would you like to suffer that?"

Bill turned, stared at Mewtwo, and looked away when the Pokemon coldly returned his gaze. Bill smirked and said, "Nope. It's a good thing I have this, then."

Before anyone could react, Bill slipped a pill out of his pocket and stuffed it immediately into his mouth. He had swallowed it when Giovanni grabbed him by his shirt and lifted him off the ground.

"What did you do?" Giovanni demanded.

Bill still retained his smirk. "Took…took a pill…that's killing me…guess you…you still need to find some…somewhere else to get that info…"

Bill's eyes became glazed, and he became deadweight in Giovanni's grasp. He dropped the corpse to the ground and took a step back. If this group was so determined to remain secretive to have captured operatives kill themselves, then he'd have to search extremely hard to find them.

He looked up at Proton and ordered, "Take multiple squads and search Hoenn and anywhere else in the vicinity. I want them found. Now."

-Line-

Brad took deep breaths as he leaned against the a tree. His Bagon stood beside him, also panting. They had just gotten away from the Beedrill and had paused here to rest.

"I think we lost them," Brad said, sighing. "Wish we had the chance to catch one. Oh well."

Brad sighed, then heard faint cries from somewhere nearby. Brad and Bagon followed the cries until they came upon a small Pichu lying on the ground. It was uninjured, but it looked extremely afraid and lonely. Brad approached it steadily, then bent down beside it and said, "Hello."

The Pichu's head jerked up and it suddenly zapped him. Brad cried out and fell on his back. The Pichu growled and jumped up, landing on Brad's belly and zapping him. His Bagon rushed in and chomped down on Pichu with Bite. It cried out and tried to electrocute Bagon, but the Dragon-type tossed it away. It then approached Pichu, glaring at it. Brad got up and snapped, "What was that for, huh? I was only trying to help!"

The Pichu growled and prepared more electricity, but then Bagon charged and used Bite again, causing Pichu to cry out in pain. When Bagon released it, the little Pokemon suddenly began crying.

"Oh, for Arceus's sake, what are we going to do now?" Brad said. "That crying might bring about its parents, not to mention those Beedrill. What are we going to do?"

Bagon shrugged. Brad then snapped his fingers and pulled out an Oran Berry. He carefully approached the crying Pichu and set down the Berry, then stepped back, awaiting a reaction. He did not have to wait long. Pichu stopped crying, sniffed the Berry, nibbled it, then began eating it with more enjoyment. When it was through, the Pichu crawled up Brad's leg and ended up on his shoulder. Pichu rubbed its cheek on Brad's, squealing in delight. "Hey, what would you say to being my Pokemon?" Brad asked.

Pichu paused, then nodded. Brad touched it with a PokeBall, allowing it to jump in, then released it again. Pichu jumped onto his shoulder, and Bagon jumped onto the other.

"All right, guys. Let's get going!" Brad declared. His two partners nodded in agreement, and Brad set off again, walking through the forest.


End file.
